By any traditional definition of "workstation" it is not one. It is no more a workstation than the Mini is. Both need additional products to make them functional as such.
I don't think that this change is different, in spirit, from some of the changes that Apple has pushed in the past. Apple tends to jettison things that it thinks are no longer relevant to the future, e.g. SCSI, ADB, Serial ports, etc. When Apple went USB-only on the original iMac, it was a controversial move, because there wasn't much in the way of a USB device market at that point in time. Fast forward a year or so, and there were more USB devices than you could shake a mouse at. I see the Mac Pro "sneak peek" as a warning shot across the bow of the peripheral manufacturers. If manufacturers get on board with Thunderbolt, it's a pretty interesting future, I think.
My workflow already uses a combination of a fast boot/swap drive, FW800 and NAS for storage, so that won't change much with a new Mac Pro, other than needing a TB->FW adaptor somewhere (at a cost of $29 from Apple.) I'm a firm believer in the concept of storage living outside of my "compute core." I've changed computers with barely a hitch because my data lived somewhere else.
Many PCIe cards will already work in an expansion chassis. Many will not. I believe this is mostly a driver issue, other than the rare card that needs more bandwidth than Thunderbolt provides. If you are someone who needs that third (or fifth) high speed graphics card, the new Mac Pro is not for you. But realistically, what percentage of the potential market for this sort of machine is in that segment? I imagine that most PCIe cards will be made to work in an expansion chassis, or a Thunderbolt alternative will appear.
That said, I'm stuck waiting for MOTU to come up with a Thunderbolt solution for their PCI line (e.g. 2408mk3, HD192). Their adaptor card, the PCIe-424, does NOT work in an expansion chassis. If MOTU doesn't come up with a solution for using their PCI line, the ripple effect of me moving to a new Mac Pro would involve replacing audio interfaces, and my digital mixer. The follow-on costs would probably end up being more than the MacPro. I'm optimistic that MOTU, like most manufacturers will get its act together regarding Thunderbolt.
Summing up, if Apple & Intel are successful in their gamble to push the world towards Thunderbolt, in a year or so, we'll think that compute cores like the Mac Pro are the natural order. We'll wonder what all the fuss was about. Isn't this the way computers have always been?